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Tran CS, Kersten J, Yan J, Breinig M, Huth T, Poth T, Colasanti O, Riedl T, Faure-Dupuy S, Diehl S, Verhoye L, Li TF, Lingemann M, Schult P, Ahlén G, Frelin L, Kühnel F, Vondran FWR, Breuhahn K, Meuleman P, Heikenwälder M, Schirmacher P, Bartenschlager R, Laketa V, Roessler S, Tschaharganeh DF, Sällberg M, Lohmann V. Phosphatidylinositol 4-Kinase III Alpha Governs Cytoskeletal Organization for Invasiveness of Liver Cancer Cells. Gastroenterology 2024; 167:522-537. [PMID: 38636680 DOI: 10.1053/j.gastro.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND & AIMS High expression of phosphatidylinositol 4-kinase III alpha (PI4KIIIα) correlates with poor survival rates in patients with hepatocellular carcinoma. In addition, hepatitis C virus (HCV) infections activate PI4KIIIα and contribute to hepatocellular carcinoma progression. We aimed at mechanistically understanding the impact of PI4KIIIα on the progression of liver cancer and the potential contribution of HCV in this process. METHODS Several hepatic cell culture and mouse models were used to study the functional importance of PI4KIIIα on liver pathogenesis. Antibody arrays, gene silencing, and PI4KIIIα-specific inhibitor were applied to identify the involved signaling pathways. The contribution of HCV was examined by using HCV infection or overexpression of its nonstructural protein. RESULTS High PI4KIIIα expression and/or activity induced cytoskeletal rearrangements via increased phosphorylation of paxillin and cofilin. This led to morphologic alterations and higher migratory and invasive properties of liver cancer cells. We further identified the liver-specific lipid kinase phosphatidylinositol 3-kinase C2 domain-containing subunit gamma (PIK3C2γ) working downstream of PI4KIIIα in regulation of the cytoskeleton. PIK3C2γ generates plasma membrane phosphatidylinositol 3,4-bisphosphate-enriched, invadopodia-like structures that regulate cytoskeletal reorganization by promoting Akt2 phosphorylation. CONCLUSIONS PI4KIIIα regulates cytoskeleton organization via PIK3C2γ/Akt2/paxillin-cofilin to favor migration and invasion of liver cancer cells. These findings provide mechanistic insight into the contribution of PI4KIIIα and HCV to the progression of liver cancer and identify promising targets for therapeutic intervention.
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Affiliation(s)
- Cong Si Tran
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Julia Kersten
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Jingyi Yan
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden; Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden
| | - Marco Breinig
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thorben Huth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Tanja Poth
- Center for Model System and Comparative Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ombretta Colasanti
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany
| | - Suzanne Faure-Dupuy
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany; Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Stefan Diehl
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Lieven Verhoye
- Laboratory of Liver Infectious Diseases, Ghent University, Ghent, Belgium
| | - Teng-Feng Li
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Marit Lingemann
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Philipp Schult
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Gustaf Ahlén
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden; Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden
| | - Lars Frelin
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden; Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden
| | - Florian Kühnel
- Department of Gastroenterology, Hepatology, Infectiology, and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Florian W R Vondran
- Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover, Hannover, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Philip Meuleman
- Laboratory of Liver Infectious Diseases, Ghent University, Ghent, Belgium
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany; The M3 Research Institute, Medical Faculty Tübingen, Tübingen, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- DZIF, Partner Site Heidelberg, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, DKFZ, Heidelberg, Germany; Department of Infectious Diseases, Molecular Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Vibor Laketa
- DZIF, Partner Site Heidelberg, Heidelberg, Germany; Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany
| | - Darjus Felix Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matti Sällberg
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden; Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Section Virus-Host Interactions, Center for Integrative Infectious Disease Research, Heidelberg University, Medical Faculty Heidelberg, Heidelberg, Germany; DZIF, Partner Site Heidelberg, Heidelberg, Germany.
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Liu Q, Lin Z, Yue M, Wu J, Li L, Huang D, Fang Y, Zhang X, Hao T. Identification and validation of ferroptosis related markers in erythrocyte differentiation of umbilical cord blood-derived CD34 + cell by bioinformatic analysis. Front Genet 2024; 15:1365232. [PMID: 39139819 PMCID: PMC11319168 DOI: 10.3389/fgene.2024.1365232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Ferroptosis has been observed to play an important role during erythrocyte differentiation (ED). However, the biological gene markers and ferroptosis mechanisms in ED remain unknown. We downloaded the datasets of ED in human umbilical cord blood-derived CD34+ cells from the Gene Expression Omnibus database. Using median differentiation time, the sample was categorized into long and short groups. The differentially expressed ferroptosis-related genes (DE-FRGs) were screened using differential expression analysis. The enrichment analyses and a protein-protein interaction (PPI) network were conducted. To predict the ED stage, a logistic regression model was constructed using the least absolute shrinkage and selection operator (LASSO). Overall, 22 DE-FRGs were identified. Ferroptosis-related pathways were enriched using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. Gene Set Enrichment Analysis and Gene Set Variation Analysis revealed the primary involvement of DE-FRGs in JAK-STAT, MAPK, PI3K-AKT-mTORC1, WNT, and NOTCH signaling pathways. Ten-hub DE-FRGs were obtained using PPI analysis. Furthermore, we constructed mRNA-microRNA (miRNA) and mRNA-transcription factor networks. Immune cell infiltration levels differed significantly during ED. LASSO regression analysis established a signature using six DE-FRGs (ATF3, CDH2, CHAC1, DDR2, DPP4, and GDF15) related to the ED stage. Bioinformatic analyses identified ferroptosis-associated genes during ED, which were further validated. Overall, we identified ferroptosis-related genes to predict their correlations in ED. Exploring the underlying mechanisms of ferroptosis may help us better understand pathophysiological changes in ED and provide new evidence for clinical transformation.
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Affiliation(s)
- Qian Liu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Ze Lin
- Shantou University Medical College, Shantou, Guangdong, China
| | - Minghui Yue
- Shantou University Medical College, Shantou, Guangdong, China
| | - Jianbo Wu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Lei Li
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Daqi Huang
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Yipeng Fang
- Department of Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Zhang
- Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Molecular Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Tao Hao
- Department of Colorectal Surgery, Binzhou Medical University Hospital, Binzhou, Shandong, China
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Wang Z, Han X, Su X, Yang X, Wang X, Yan J, Qian Q, Wang H. Analysis of key circRNA events in the AOP framework of TCS acting on zebrafish based on the data-driven. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116507. [PMID: 38838465 DOI: 10.1016/j.ecoenv.2024.116507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Triclosan (TCS) is a broad-spectrum antibiotic widely used in various personal care products. Research has found that exposure to TCS can cause toxic effects on organisms including neurotoxicity, cardiotoxicity, disorders of lipid metabolism, and abnormal vascular development, and the corresponding toxic mechanisms are gradually delving into the level of abnormal expression of miRNA regulating gene expression. Although the downstream mechanism of TCS targeting miRNA abnormal expression to induce toxicity is gradually improving, its upstream mechanism is still in a fog. Starting from the abnormal expression data of circRNA in zebrafish larvae induced by TCS, this study conducted a hierarchical analysis of the expression levels of all circRNAs, differential circRNAs, and trend circRNAs, and identified 29 key circRNA events regulating miRNA abnormal expression. In combination with GO and KEGG, the effects of TCS exposure were analyzed from the function and signaling pathway of the corresponding circRNA host gene. Furthermore, based on existing literature evidence about the biological toxicity induced by TCS targeting miRNA as data support, a competing endogenous RNAs (ceRNA) network characterizing the regulatory relationship between circRNA and miRNA was constructed and optimized. Finally, a comprehensive Adverse Outcome Pathway (AOP) framework of multiple levels of events including circRNA, miRNA, mRNA, pathway, and toxicity endpoints was established to systematically elucidate the toxic mechanism of TCS. Moreover, the rationality of the AOP framework was verified from the expression level of miRNA and adverse outcomes such as neurotoxicity, cardiotoxicity, oxidative stress, and inflammatory response by knockdown of circRNA48. This paper not only provides the key circRNA events for exploring the upstream mechanism of miRNA regulating gene expression but also provides an AOP framework for comprehensively demonstrating the toxicity mechanism of TCS on zebrafish, which is a theoretical basis for subsequent hazard assessment and prevention and control of TCS.
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Affiliation(s)
- Zejun Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xiaowen Han
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xincong Su
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xiao Yang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xuedong Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jin Yan
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Qiuhui Qian
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Huili Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
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Xu Y, Guo R, Huang T, Guo C. miRNA-7145-cuedc2 axis controls hematopoiesis through JAK1/STAT3 signaling pathway. Cell Death Discov 2024; 10:209. [PMID: 38697957 PMCID: PMC11066045 DOI: 10.1038/s41420-024-01977-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Hematopoiesis ensures tissue oxygenation, and remodeling as well as immune protection in vertebrates. During embryogenesis, hemangioblasts are the source of all blood cells. Gata1a and pu.1 are co-expressed in hemangioblasts before hemangioblasts are differentiated into blood cells. However, the genes that determine the differentiation of hemangioblasts into myeloid or erythroid cell lineages have not been fully uncovered. Here we showed that miRNA-7145, a miRNA with previously unknown function, was enriched in erythrocytes at the definitive wave, but not expressed in myeloid cells. Overexpression and loss-of-function analysis of miRNA-7145 revealed that miRNA-7145 functions as a strong inhibitor for myeloid progenitor cell differentiation while driving erythropoiesis during the primitive wave. Furthermore, we confirmed that cuedc2 is one of miRNA-7145 targeted-genes. Overexpression or knock-down of cuedc2 partially rescues the phenotype caused by miRNA-7145 overexpression or loss-of-function. As well, overexpression and loss-of-function analysis of cuedc2 showed that cuedc2 is required for myelopoiesis at the expense of erythropoiesis. Finally, we found that overexpression of zebrafish cuedc2 in 293 T cell inhibits the JAK1/STAT3 signaling pathway. Collectively, our results uncover a previously unknown miRNA-7145-cuedc2 axis, which regulate hematopoiesis through inhibiting the JAK1/STAT3 signaling pathway.
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Affiliation(s)
- Yongsheng Xu
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China.
| | - Rui Guo
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Tao Huang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Chunming Guo
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China.
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5
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Bura A, Čabrijan S, Đurić I, Bruketa T, Jurak Begonja A. A Plethora of Functions Condensed into Tiny Phospholipids: The Story of PI4P and PI(4,5)P 2. Cells 2023; 12:1411. [PMID: 37408244 DOI: 10.3390/cells12101411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Phosphoinositides (PIs) are small, phosphorylated lipids that serve many functions in the cell. They regulate endo- and exocytosis, vesicular trafficking, actin reorganization, and cell mobility, and they act as signaling molecules. The most abundant PIs in the cell are phosphatidylinositol-4-monophosphate (PI4P) and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. PI4P is mostly localized at the Golgi apparatus where it regulates the anterograde trafficking from the Golgi apparatus to the plasma membrane (PM), but it also localizes at the PM. On the other hand, the main localization site of PI(4,5)P2 is the PM where it regulates the formation of endocytic vesicles. The levels of PIs are regulated by many kinases and phosphatases. Four main kinases phosphorylate the precursor molecule phosphatidylinositol into PI4P, divided into two classes (PI4KIIα, PI4KIIβ, PI4KIIIα, and PI4KIIIβ), and three main kinases phosphorylate PI4P to form PI(4,5)P2 (PI4P5KIα, PI4P5KIβ, and PI4P5KIγ). In this review, we discuss the localization and function of the kinases that produce PI4P and PI(4,5)P2, as well as the localization and function of their product molecules with an overview of tools for the detection of these PIs.
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Affiliation(s)
- Ana Bura
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Sara Čabrijan
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Iris Đurić
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Tea Bruketa
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Antonija Jurak Begonja
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
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McPhail JA, Burke JE. Molecular mechanisms of PI4K regulation and their involvement in viral replication. Traffic 2023; 24:131-145. [PMID: 35579216 DOI: 10.1111/tra.12841] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Lipid phosphoinositides are master signaling molecules in eukaryotic cells and key markers of organelle identity. Because of these important roles, the kinases and phosphatases that generate phosphoinositides must be tightly regulated. Viruses can manipulate this regulation, with the Type III phosphatidylinositol 4-kinases (PI4KA and PI4KB) being hijacked by many RNA viruses to mediate their intracellular replication through the formation of phosphatidylinositol 4-phosphate (PI4P)-enriched replication organelles (ROs). Different viruses have evolved unique approaches toward activating PI4K enzymes to form ROs, through both direct binding of PI4Ks and modulation of PI4K accessory proteins. This review will focus on PI4KA and PI4KB and discuss their roles in signaling, functions in membrane trafficking and manipulation by viruses. Our focus will be the molecular basis for how PI4KA and PI4KB are activated by both protein-binding partners and post-translational modifications, with an emphasis on understanding the different molecular mechanisms viruses have evolved to usurp PI4Ks. We will also discuss the chemical tools available to study the role of PI4Ks in viral infection.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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Gopal A, Ibrahim R, Fuller M, Umlandt P, Parker J, Tran J, Chang L, Wegrzyn-Woltosz J, Lam J, Li J, Lu M, Karsan A. TIRAP drives myelosuppression through an Ifnγ-Hmgb1 axis that disrupts the endothelial niche in mice. J Exp Med 2022; 219:212987. [PMID: 35089323 PMCID: PMC8932532 DOI: 10.1084/jem.20200731] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/15/2021] [Accepted: 12/16/2021] [Indexed: 12/31/2022] Open
Abstract
Inflammation is associated with bone marrow failure syndromes, but how specific molecules impact the bone marrow microenvironment is not well elucidated. We report a novel role for the miR-145 target, Toll/interleukin-1 receptor domain containing adaptor protein (TIRAP), in driving bone marrow failure. We show that TIRAP is overexpressed in various types of myelodysplastic syndromes (MDS) and suppresses all three major hematopoietic lineages. TIRAP expression promotes up-regulation of Ifnγ, leading to myelosuppression through Ifnγ-Ifnγr–mediated release of the alarmin, Hmgb1, which disrupts the bone marrow endothelial niche. Deletion of Ifnγ blocks Hmgb1 release and is sufficient to reverse the endothelial defect and restore myelopoiesis. Contrary to current dogma, TIRAP-activated Ifnγ-driven bone marrow suppression is independent of T cell function or pyroptosis. In the absence of Ifnγ, TIRAP drives myeloproliferation, implicating Ifnγ in suppressing the transformation of MDS to acute leukemia. These findings reveal novel, noncanonical roles of TIRAP, Hmgb1, and Ifnγ in the bone marrow microenvironment and provide insight into the pathophysiology of preleukemic syndromes.
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Affiliation(s)
- Aparna Gopal
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Rawa Ibrahim
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Patricia Umlandt
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jeremy Parker
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jessica Tran
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Linda Chang
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joanna Wegrzyn-Woltosz
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey Lam
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jenny Li
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Melody Lu
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Ware TB, Hsu KL. Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study. Curr Opin Chem Biol 2021; 65:101-108. [PMID: 34311404 PMCID: PMC8671151 DOI: 10.1016/j.cbpa.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/24/2021] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
Advancements in chemical proteomics and mass spectrometry lipidomics are providing new opportunities to understand lipid kinase activity, specificity, and regulation on a global cellular scale. Here, we describe recent developments in chemical biology of lipid kinases with a focus on those members that phosphorylate diacylglycerols. We further discuss future implications of how these mass spectrometry-based approaches can be adapted for studies of additional lipid kinase members with the aim of bridging the gap between protein and lipid kinase-focused investigations.
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Affiliation(s)
- Timothy B Ware
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, United States; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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9
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Using the Zebrafish as a Genetic Model to Study Erythropoiesis. Int J Mol Sci 2021; 22:ijms221910475. [PMID: 34638816 PMCID: PMC8508994 DOI: 10.3390/ijms221910475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/18/2021] [Accepted: 09/25/2021] [Indexed: 11/30/2022] Open
Abstract
Vertebrates generate mature red blood cells (RBCs) via a highly regulated, multistep process called erythropoiesis. Erythropoiesis involves synthesis of heme and hemoglobin, clearance of the nuclei and other organelles, and remodeling of the plasma membrane, and these processes are exquisitely coordinated by specific regulatory factors including transcriptional factors and signaling molecules. Defects in erythropoiesis can lead to blood disorders such as congenital dyserythropoietic anemias, Diamond–Blackfan anemias, sideroblastic anemias, myelodysplastic syndrome, and porphyria. The molecular mechanisms of erythropoiesis are highly conserved between fish and mammals, and the zebrafish (Danio rerio) has provided a powerful genetic model for studying erythropoiesis. Studies in zebrafish have yielded important insights into RBC development and established a number of models for human blood diseases. Here, we focus on latest discoveries of the molecular processes and mechanisms regulating zebrafish erythropoiesis and summarize newly established zebrafish models of human anemias.
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10
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Pseudogenes and their potential functions in hematopoiesis. Exp Hematol 2021; 103:24-29. [PMID: 34517065 DOI: 10.1016/j.exphem.2021.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/01/2021] [Accepted: 09/05/2021] [Indexed: 11/24/2022]
Abstract
Pseudogenes are DNA regions comprising defective copies of functional genes, the majority of which were generated by RNA- or DNA-level duplications. They exist across almost all forms of life and account for about one-quarter of the annotated genes in the human genome. Although these have been considered nonfunctional for decades, a growing number of pseudogenes have been found to be transcribed and to play crucial regulatory roles. Accumulating evidence indicates that they regulate gene expression through molecular interactions at the protein, RNA, and DNA levels. However, pseudogenes are often excluded in multiple genomewide analyses and functional screening, and their biological activities remain to be systematically disclosed. Here, we summarize the features of and progress of research on pseudogenes, in addition to discussing what is unknown about these genetic elements. Our previous findings, together with evidence of their poor conservation, prompted us to propose that pseudogenes may contribute to primate- or human-specific regulation, especially in hematopoiesis.
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Transposon Insertion Mutagenesis in Mice for Modeling Human Cancers: Critical Insights Gained and New Opportunities. Int J Mol Sci 2020; 21:ijms21031172. [PMID: 32050713 PMCID: PMC7036786 DOI: 10.3390/ijms21031172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023] Open
Abstract
Transposon mutagenesis has been used to model many types of human cancer in mice, leading to the discovery of novel cancer genes and insights into the mechanism of tumorigenesis. For this review, we identified over twenty types of human cancer that have been modeled in the mouse using Sleeping Beauty and piggyBac transposon insertion mutagenesis. We examine several specific biological insights that have been gained and describe opportunities for continued research. Specifically, we review studies with a focus on understanding metastasis, therapy resistance, and tumor cell of origin. Additionally, we propose further uses of transposon-based models to identify rarely mutated driver genes across many cancers, understand additional mechanisms of drug resistance and metastasis, and define personalized therapies for cancer patients with obesity as a comorbidity.
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Cell type-specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders. Transl Psychiatry 2019; 9:1. [PMID: 30664621 PMCID: PMC6341096 DOI: 10.1038/s41398-018-0355-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/26/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Posttraumatic stress disorder (PTSD), a chronic disorder resulting from severe trauma, has been linked to immunologic dysregulation. Gene expression profiling has emerged as a promising tool for understanding the pathophysiology of PTSD. However, to date, all but one gene expression study was based on whole blood or unsorted peripheral blood mononuclear cell (PBMC), a complex tissue consisting of several populations of cells. The objective of this study was to utilize RNA sequencing to simultaneously profile the gene expression of four immune cell subpopulations (CD4T, CD8T, B cells, and monocytes) in 39 World Trade Center responders (20 with and 19 without PTSD) to determine which immune subsets play a role in the transcriptomic changes found in whole blood. Transcriptome-wide analyses identified cell-specific and shared differentially expressed genes across the four cell types. FKBP5 and PI4KAP1 genes were consistently upregulated across all cell types. Notably, REST and SEPT4, genes linked to neurodegeneration, were among the top differentially expressed genes in monocytes. Pathway analyses identified differentially expressed gene sets involved in mast cell activation and regulation in CD4T, interferon-beta production in CD8T, and neutrophil-related gene sets in monocytes. These findings suggest that gene expression indicative of immune dysregulation is common across several immune cell populations in PTSD. Furthermore, given notable differences between cell subpopulations in gene expression associated with PTSD, the results also indicate that it may be valuable to analyze different cell populations separately. Monocytes may constitute a key cell type to target in research on gene expression profile of PTSD.
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Dornan GL, Dalwadi U, Hamelin DJ, Hoffmann RM, Yip CK, Burke JE. Probing the Architecture, Dynamics, and Inhibition of the PI4KIIIα/TTC7/FAM126 Complex. J Mol Biol 2018; 430:3129-3142. [PMID: 30031006 DOI: 10.1016/j.jmb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 11/16/2022]
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα) is the lipid kinase primarily responsible for generating the lipid phosphatidylinositol 4-phosphate (PI4P) at the plasma membrane, which acts as the substrate for generation of the signaling lipids PIP2 and PIP3. PI4KIIIα forms a large heterotrimeric complex with two regulatory partners, TTC7 and FAM126. We describe using an integrated electron microscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) approach to probe the architecture and dynamics of the complex of PI4KIIIα/TTC7/FAM126. HDX-MS reveals that the majority of the PI4KIIIα sequence was protected from exchange in short deuterium pulse experiments, suggesting presence of secondary structure, even in putative unstructured regions. Negative stain electron microscopy reveals the shape and architecture of the full-length complex, revealing an overall dimer of PI4KIIIα/TTC7/FAM126 trimers. HDX-MS reveals conformational changes in the TTC7/FAM126 complex upon binding PI4KIIIα, including both at the direct TTC7-PI4KIIIα interface and at the putative membrane binding surface. Finally, HDX-MS experiments of PI4KIIIα bound to the highly potent and selective inhibitor GSK-A1 compared to that bound to the non-specific inhibitor PIK93 revealed substantial conformational changes throughout an extended region of the kinase domain. Many of these changes were distant from the putative inhibitor binding site, showing a large degree of allosteric conformational changes that occur upon inhibitor binding. Overall, our results reveal novel insight into the regulation of PI4KIIIα by its regulatory proteins TTC7/FAM126, as well as additional dynamic information on how selective inhibition of PI4KIIIα is achieved.
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Affiliation(s)
- Gillian L Dornan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2.
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